Poster presented in the 11th Rosaceae Genomics Conference (Nelson, New Zealand - March 2023)
References
Taniguti, C. H., Taniguti, L. M., Amadeu, R. R., Lau, J., de Siqueira Gesteira, G., De, T., Oliveira, P., Ferreira, G. C., Da, G., Pereira, S., Byrne, D., Mollinari, M., Riera-Lizarazu, O., & Franco Garcia, A. A. (n.d.). Developing best practices for genotyping-by-sequencing analysis using linkage maps as benchmarks. bioRxiv. https://doi.org/10.1101/2022.11.24.517847
Taniguti, C. H., de Siqueira Gesteira, G., Lau, J., da Silva Pereira, G., Zeng, Z.-B., Byrne, D., Riera-Lizarazu, O., & Mollinari, M. (2022). VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis. Journal of Open Source Software, 7(74), 4242. https://doi.org/10.21105/joss.04242
Margarido, G. R. A., Souza, A. P., & Garcia, A. A. F. (2007). OneMap: software for genetic mapping in outcrossing species. Hereditas, 144(3), 78–79. https://doi.org/10.1111/j.2007.0018-0661.02000.x
Mollinari, M., & Garcia, A. A. F. (2019). Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3: Genes|Genomes|Genetics, 9(10), 3297–3314. https://doi.org/10.1534/g3.119.400378
Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., & Mitchell, S. E. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6(5), e19379. https://doi.org/10.1371/journal.pone.0019379
Glaubitz, J. C., Casstevens, T. M., Lu, F., Harriman, J., Elshire, R. J., Sun, Q., & Buckler, E. S. (2014). TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS ONE, 9(2), 1–11. https://doi.org/10.1371/journal.pone.0090346
Voss, K., Gentry, J., & Auwera, G. van der. (2017). Full-stack genomics pipelining with GATK4+ WDL+ Cromwell [version 1; not peer reviewed]. F1000Research, 4. https://doi.org/10.7490/f1000research.1114631.1
Yu, Z., Du, F., Ban, R., & Zhang, Y. (2020). SimuSCoP: Reliably simulate Illumina sequencing data based on position and context dependent profiles. BMC Bioinformatics, 21(1), 1–18. https://doi.org/10.1186/s12859-020-03665-5
Rivera-Colón, A. G., Rochette, N. C., & Catchen, J. M. (2020). Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data. Molecular Ecology Resources, March, 1–16. https://doi.org/10.1111/1755- 0998.13163
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows– Wheeler transform. Bioinformatics, 25(14), 1754–1760. https://doi.org/10.1093/bioinformatics/btp324
van der Auwera, G., & O’Connor, B. (2020). Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. O’Reilly Media, Incorporated. https://books.google.com.br/books?id=wwiCswEACAAJ
Garrison, E., & Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. ArXiv E-Prints, 9. https://doi.org/1207.3907
Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). Genotyping Polyploids from Messy Sequencing Data. Genetics, 210(3), 789–807. https://doi.org/10.1534/genetics.118.301468
Clark, L. v., Lipka, A. E., & Sacks, E. J. (2019). polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids. G3: Genes|Genomes|Genetics, 9(March), g3.200913.2018. https://doi.org/10.1534/g3.118.200913
Serang, O., Mollinari, M., & Garcia, A. A. F. (2012). Efficient exact maximum a posteriori computation for bayesian SNP genotyping in polyploids. PLoS ONE, 7(2), 1– 13. https://doi.org/10.1371/journal.pone.0030906
Merkel, D. (2014). Docker : Lightweight Linux Containers for Consistent Development and Deployment Docker : a Little Background Under the Hood. Linux Journal, 2014(239), 2–7.
Kurtzer, G. M., Sochat, V., & Bauer, M. W. (2017). Singularity: Scientific containers for mobility of compute. PLOS ONE, 12(5), e0177459. https://doi.org/10.1371/journal.pone.0177459